Scoring a Search Amino acid searches are easier than nucleotide - but data is often nucleotide Quality of results depends on appropriate algorithms - and well-maintained databases Alignments are given scores - looking for alignments w/ higher score than would be expected from a random match Can estimate the probability of two random sequences aligning with a score ≥ S, the expectation or E-value The E-value is the number of alignments w/ a score of at least S that would be expected by chance alone in searching a complete dataset of n sequences, from 0 to n An E-value of 3 means you would expect 3 such matches, 10 -29 means very few 11:28 AM